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It features a unique and innovative weapons system, with seven weapons available at any time. The player has three buttons to control the weapons; the weapon fired depends on the combination of buttons pressed. According to producer Hiroshi Iuchi, the main inspiration for the game's design was Image Fight, an arcade game by Irem from 1988.[2]

Unlike in most other shoot 'em ups, there are no power-ups. All weapons are available from the start. Weapons can 'level up', however, becoming more powerful as the player uses them to score points. There are a selection of 7 weapons that can be used at any given time:

The game is designed so that there is almost always a 'right' weapon for any situation. The bosses in the game are designed so that they have multiple 'sections' which, if all destroyed before the 'core' of the boss, will award the players with point bonuses. Being able to apply the right weapons on any different boss is key to obtaining these bonuses. For example, a boss may have two sections located on either side of the screen. You could immediately go up to one and begin shooting it with a vulcan, or you could hover in the centre and hit both at the same time with the side bombs. This would increase your chance of obtaining the bonus before the time limit runs out and the boss self-destructs.

The game rewards players for "chaining" enemies of just one of three colors, red, blue, or yellow. Whenever the player kills three enemies that are of the same color, they can obtain a points bonus. This also facilitates faster upgrading of weapons.

In the arcade mode, the game's first level is stage 3. At the end of stage 3, the player can choose to continue at stage 2 or stage 4. Both stages lead to stage 5, then stage 6, and the finale at stage 1. This is true to the story's chronology; for example, the events of stage 2 occurred a year before stage 3. In the Saturn version, the player is forced to play all of the stages, starting at stage 3, to stage 2, then 4 through 6 and 1.

An octahedron-shaped artifact called the Stone-Like, along with a non-functioning robot, has been unearthed. Earth's secretary of defense, Chief Igarashi, orders the Stone-Like to be examined. Meanwhile, up in Earth's atmosphere, inside the spaceship Tetra, Commander Tengai issues Buster, Reana and Guy to test out the three new Silvergun prototype fighter crafts. Back on Earth, Igarashi relays information on the Stone-Like and the robot, claiming it has the serial number 00104, exactly the same number of the robot aboard the Tetra, CREATOR 00104. Tengai cannot believe this be just a coincidence (partly due to Igarashi proving that it is, indeed the same robot), and has the three Silvergun pilots on standby. Suddenly, the Stone-Like starts to act up and destroys the facility containing it. As it overwhelms the Earth defense forces, the Stone-Like wipes out all life on Earth in a magnificent flash. Only the crew of the Tetra remain unharmed, as they were in satellite orbit. One year after the Stone-Like destroyed Earth, the Tetra, running low on food and fuel supplies, makes its return to Earth.

The story is now told non-linearly, beginning with the third stage of the game, entitled Return. The Tetra flies back to Earth, and the three pilots, in their respective Silverguns, are sent out to investigate. Stage 2, Reminiscence, is actually a flashback sequence, where the Tetra and the Silverguns head to the Earth defense headquarters, where Chief Igarashi is, prior to the Stone-Like's attack. Knowing it's impossible to stop the Stone-Like, Igarashi has the Tetra and the Silverguns to make for satellite orbit, and evade the Stone-Like. The escape is successful, but the same cannot be said for Earth and its inhabitants.

Back in the present, the Stone-Like, now aware of the Tetra and Silverguns' presence, uses its power and commands its own manufactured weapons to destroy them. Stage 4, known as Evasion, now takes place. Seeing a need to know more about the Stone-Like, Tengai has Creator, the robot aboard the Tetra, to head for the Earth defense headquarters and gather information about it, while the Tetra and the Silverguns hold off the Stone-Like's forces. However, the Stone-Like sees through their plan and heads straight for the headquarters as well. Stage 5, Victim, begins, as two towering battleships lumber over the headquarters, intending to prevent Creator from succeeding its mission. The Silverguns hastily destroys the cruisers, but the Stone-Like appears and levels the headquarters. Just before the building collapses, Tengai pilots the Tetra and holds up the structure from falling, allowing Creator to board Reana's Silvergun to safety. Catching the Stone-Like off-guard, Gai goes on a suicidal run and attempts to destroy the artifact, but fails to do so, as his Silvergun vanishes upon contact with it. Tengai orders Buster and Reana to head for space, while he makes a last-ditch effort and attempt to stall the Stone-Like, just as Gai did. With all seemingly lost, Buster persuades Reana to join him and try to destroy the Stone-Like. Before they head out into the space, Creator asks that they leave it one thing from them...

The Stone-Like, having located Buster and Reana, engages them in space combat, while briefly explaining that because of humanity's constant nature to war and destruction, it had to bring about the apocalypse. Stage 6, The Origin, concludes with the Stone-Like, having been defeated, now transports the two Silverguns and its pilots back in time, to the year 100,000 BC. Stage 1, Link, has the Stone-Like unleash its power in a cataclysmic explosion. As Buster and Reana make an attempt to escape the blast, they are swallowed up in the blinding light, seemingly destroyed. The ending concludes with Creator, 20 years into the future, having secluded itself inside an underground facility on Earth, now brimming with life again, creating a clone of Buster and Reana, from their strands of hair, the thing that he asked from both of them. The Stone-Like is now deactivated, its power exhausted from the last battle.

In its last moments before its energy fades, Creator explains that the Stone-Like is the guardian of Earth, and sees to it the advancement of the planet, its inhabitants and their way of living. If it deems that things must start over, the Stone-Like will destroy Earth and recreate it again, until humanity realize their nature and change before the Stone-Like delivers the consequences. Creator's purpose was always to ensure that mankind will survive, through their clones, and with these words, Creator stops functioning. As the story ends, the Buster and Reana clone start to wake from their cloning tubes.

The story of Radiant Silvergun is only available in the Saturn Mode of the Sega Saturn version of the game. Arcade Mode and the original arcade version of Radiant Silvergun do not include any cutscenes or dialog save for a slide show at the end of the game consisting of stills from the ending video.

A port of the game with enhanced high definition visuals was released on the Xbox 360's Xbox Live Arcade service on September 14, 2011. Rather than emulate the Sega Saturn, the source code was used to port the game to the Xbox 360's hardware. Sprites were redrawn in high definition with an optional blooming effect, true alpha blending implemented (buggy and therefore limited on Saturn and Titan hardware) and a post-process filter applied to enhance the look of the game. Options are included to disable any or all of these graphical enhancements, allowing players to enjoy the game as it originally appeared if they so desire. Like the Xbox Live Arcade port of Ikaruga, the game's original 4:3 playing field runs pillarboxed in 16:9 aspect ratio and moves UI elements like player score, weapon level, and chain counter (new to this port of the game) to the border area with the new HUD. However, the game's original HUD can also be used if desired. In addition, the anime cut-scenes introduced in the Sega Saturn version of the game return with subtitles based on the Xbox 360's system language. Another special feature of the Xbox Live Arcade port of Radiant Silvergun includes a secret "Ikaruga Mode" where the game uses the same scoring mechanics of its spiritual successor, which can be accessed by unlocking an achievement within Ikaruga. Finally, the game comes with the options to play local or online cooperative modes and online leaderboards with the ability to download and share replays over Xbox Live.